diff --git a/README b/README index 62855b3efdf0451346d5498b5793a483b7a16058..129a7ebd1557fb40af3d447d3e016f702b8c91c0 100644 --- a/README +++ b/README @@ -35,10 +35,13 @@ available on the Galaxy website. I merely found it too slow to do several itera especially with large sequencing datasets. Regardless, I am grateful to the Galaxy team for creating such a useful site that is rapidly approaching ubiquity. -4. Ira Hall. +4. Ira Hall, UVa. Discussion between Ira and I are largely the motivation for these tools. We are frequently tracking down impromptu ideas and these tools were largely designed to facilitate tangents. +5. Loyal Goff, CSAIL, Broad. +Many thanks to Loyal for his assistance in making BED Tools "compilable" on the SUSE platform. I appreciate your help and patience. + ===Requests=== I would be grateful to learn of any problems or suggestions you have for improving these tools. diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile index 8f9b7952d089e9f33f0e4c987ca2ae107ba5b6cf..d3a6b749be909932e9617a8c17bdf27a2140a03d 100755 --- a/src/complementBed/Makefile +++ b/src/complementBed/Makefile @@ -1,6 +1,7 @@ CXX = g++ CXXFLAGS = -O3 LDFLAGS = +LIBFLAGS = -lc UTILITIES_DIR = ../utils/ OBJ_DIR = ../../obj/ @@ -28,7 +29,7 @@ all: $(PROGRAM) $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) @echo " * linking $(PROGRAM)" - @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) + @$(CXX) $(LIBFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) $(BUILT_OBJECTS): $(SOURCES) @echo " * compiling" $(*F).cpp diff --git a/src/complementBed/complementBed.h b/src/complementBed/complementBed.h index bcdbb0b222e1b951aa46c2308ef982bc4e26b8f2..1e9cb7889861fe9c5e0199828981a0855620b849 100755 --- a/src/complementBed/complementBed.h +++ b/src/complementBed/complementBed.h @@ -5,7 +5,8 @@ #include <list> #include <iostream> #include <fstream> -#include <limits> +#include <limits.h> +#include <stdlib.h> using namespace std; diff --git a/src/coverageBed/coverageBed.h b/src/coverageBed/coverageBed.h index f3ab16d3b7d241c7d5c1d10dd7d3abf869d4f330..8504c337158fab8653b347ab38570ecac3183885 100755 --- a/src/coverageBed/coverageBed.h +++ b/src/coverageBed/coverageBed.h @@ -1,5 +1,5 @@ -#ifndef GRAPHBED_H -#define GRAPHBED_H +#ifndef COVERAGEBED_H +#define COVERAGEBED_H #include "bedFile.h" #include <vector> @@ -7,6 +7,7 @@ #include <list> #include <iostream> #include <fstream> +#include <stdlib.h> using namespace std; @@ -42,4 +43,4 @@ private: BedFile *bedA, *bedB; }; -#endif /* GRAPHBED_H */ +#endif /* COVERAGEBED_H */ diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h index 3cabeb4cea6437f86851960f3c4442a26f420689..bfc192f5cbc07fa2a678c1b472043f32587df165 100755 --- a/src/utils/bedFile/bedFile.h +++ b/src/utils/bedFile/bedFile.h @@ -8,6 +8,7 @@ #include <fstream> #include <sstream> #include <cstring> +#include <algorithm> using namespace std; diff --git a/src/utils/sequenceUtilities/sequenceUtils.h b/src/utils/sequenceUtilities/sequenceUtils.h index 1254e7e4d852d7d7da52ce6304036008055126b2..1635d49d2fa3289ed0c7f879205a0662615448f3 100644 --- a/src/utils/sequenceUtilities/sequenceUtils.h +++ b/src/utils/sequenceUtilities/sequenceUtils.h @@ -2,6 +2,8 @@ #define SEQUENCEUTILS_H #include <string> +#include <algorithm> + using namespace std; // Performs an in-place sequence reversal